For a design in that big space, I would go with a batch box, likely at least 8" size, maybe larger depending on your climate and how warm you want to keep the building. Is the 3000 sf per floor, or total? How much do you want to heat the upper floor? Can you take out a small bit of floor over the RMH area?
I would recommend a masonry bell (or two) as the most effective method for the space: a tall hollow brick box with the exhaust coming from the bottom of the hollow space so nearly all the heat is absorbed by the brick before going to the chimney. Lots of information at
https://batchrocket.eu/en/building#size .
What is the internal size of the chimney you want to use, and what condition is it in? An inspection would be a good idea before proceeding in a project of that size.